7  Tumor: Assisting cell type annotation with enrichR

7.1 Set up Seurat workspace

# Load libraries
library(data.table)
library(devtools)
library(presto)
library(glmGamPoi)
library(sctransform)
library(Seurat) 
library(tidyverse)
library(miQC)
library(SeuratWrappers)
library(flexmix)
library(SingleCellExperiment)
library(SummarizedExperiment)
library(readxl)
library(fishpond)
library(Matrix)
library(speckle)
library(scater)
library(patchwork)
library(vctrs)
library(alevinQC)
library(harmony)
library(scDblFinder)
library(cellXY)
library(enrichR)

# Set global options for Seurat v5 objects
options(Seurat.object.assay.version = 'v5')

7.2 Load sub-cluster specific marker gene table

markers <- read_tsv("Tumor_scRNA_prestoMarkers.tsv")

Rows: 100 Columns: 39
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (38): 0, 1_0, 1_1, 10, 11, 12_0, 12_1, 13, 14, 15, 16_0, 17, 18_0, 18_1,...
dbl  (1): rank

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

7.3 Run enrichR to estimate cell type annotation

dbs <- c("Tabula_Sapiens","PanglaoDB_Augmented_2021","Azimuth_Cell_Types_2021","HuBMAP_ASCTplusB_augmented_2022","Azimuth_2023","CellMarker_2024")

predictions <- NULL

for(i in colnames(markers)[-1]) {
    m <- pull(markers[,i])
    res <- enrichr(m, dbs)
    
    pred <- res %>% 
        map_dfr(~ .x %>% as_tibble(), .id = "name") %>%
        group_by(name) %>%
        slice_min(Adjusted.P.value, n=1, with_ties = F) %>%
        dplyr::select(name,Term,Adjusted.P.value) %>%
        mutate(Term = str_replace_all(str_replace_all(Term,"[ -]","_"),"_+","_")) %>%
        add_column(sub.cluster = i, .before = 1)
        
    predictions <- bind_rows(predictions, pred)     
}

Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying Tabula_Sapiens... Done.
  Querying PanglaoDB_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
  Querying HuBMAP_ASCTplusB_augmented_2022... Done.
  Querying Azimuth_2023... Done.
  Querying CellMarker_2024... Done.
Parsing results... Done.

write_tsv(predictions,"Tumor_scRNA_CellID_enrichR.tsv")

7.4 Get session info

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.10 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] enrichR_3.2                 cellXY_0.99.0              
 [3] scDblFinder_1.14.0          harmony_1.2.0              
 [5] alevinQC_1.16.1             vctrs_0.6.5                
 [7] patchwork_1.3.0             scater_1.30.1              
 [9] scuttle_1.12.0              speckle_1.0.0              
[11] Matrix_1.6-4                fishpond_2.6.2             
[13] readxl_1.4.3                SingleCellExperiment_1.24.0
[15] SummarizedExperiment_1.32.0 Biobase_2.62.0             
[17] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        
[19] IRanges_2.36.0              S4Vectors_0.40.2           
[21] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
[23] matrixStats_1.4.1           flexmix_2.3-19             
[25] lattice_0.22-6              SeuratWrappers_0.3.19      
[27] miQC_1.8.0                  lubridate_1.9.3            
[29] forcats_1.0.0               stringr_1.5.1              
[31] dplyr_1.1.4                 purrr_1.0.2                
[33] readr_2.1.5                 tidyr_1.3.1                
[35] tibble_3.2.1                ggplot2_3.5.1              
[37] tidyverse_2.0.0             Seurat_5.1.0               
[39] SeuratObject_5.0.2          sp_2.1-4                   
[41] sctransform_0.4.1           glmGamPoi_1.12.2           
[43] presto_1.0.0                Rcpp_1.0.13-1              
[45] devtools_2.4.5              usethis_3.0.0              
[47] data.table_1.16.2          

loaded via a namespace (and not attached):
  [1] fs_1.6.5                  spatstat.sparse_3.1-0    
  [3] bitops_1.0-9              httr_1.4.7               
  [5] RColorBrewer_1.1-3        profvis_0.4.0            
  [7] tools_4.3.2               utf8_1.2.4               
  [9] R6_2.5.1                  DT_0.33                  
 [11] lazyeval_0.2.2            uwot_0.2.2               
 [13] urlchecker_1.0.1          withr_3.0.2              
 [15] GGally_2.2.1              gridExtra_2.3            
 [17] progressr_0.15.1          cli_3.6.3                
 [19] spatstat.explore_3.2-6    fastDummies_1.7.3        
 [21] spatstat.data_3.1-4       ggridges_0.5.6           
 [23] pbapply_1.7-2             Rsamtools_2.18.0         
 [25] R.utils_2.12.3            WriteXLS_6.7.0           
 [27] parallelly_1.39.0         sessioninfo_1.2.2        
 [29] limma_3.58.1              RSQLite_2.3.8            
 [31] BiocIO_1.12.0             generics_0.1.3           
 [33] vroom_1.6.5               gtools_3.9.5             
 [35] ica_1.0-3                 spatstat.random_3.2-2    
 [37] ggbeeswarm_0.7.2          fansi_1.0.6              
 [39] abind_1.4-8               R.methodsS3_1.8.2        
 [41] lifecycle_1.0.4           yaml_2.3.10              
 [43] edgeR_4.0.16              SparseArray_1.2.2        
 [45] Rtsne_0.17                blob_1.2.4               
 [47] grid_4.3.2                dqrng_0.4.1              
 [49] promises_1.3.0            crayon_1.5.3             
 [51] shinydashboard_0.7.2      miniUI_0.1.1.1           
 [53] beachmat_2.18.1           cowplot_1.1.3            
 [55] KEGGREST_1.42.0           metapod_1.10.1           
 [57] pillar_1.9.0              knitr_1.45               
 [59] rjson_0.2.23              xgboost_1.7.8.1          
 [61] future.apply_1.11.3       codetools_0.2-20         
 [63] leiden_0.4.3.1            glue_1.8.0               
 [65] remotes_2.5.0             png_0.1-8                
 [67] spam_2.11-0               org.Mm.eg.db_3.18.0      
 [69] cellranger_1.1.0          gtable_0.3.6             
 [71] cachem_1.1.0              xfun_0.49                
 [73] S4Arrays_1.2.0            mime_0.12                
 [75] survival_3.7-0            bluster_1.12.0           
 [77] statmod_1.5.0             ellipsis_0.3.2           
 [79] fitdistrplus_1.2-1        ROCR_1.0-11              
 [81] nlme_3.1-166              bit64_4.5.2              
 [83] RcppAnnoy_0.0.22          irlba_2.3.5.1            
 [85] vipor_0.4.7               KernSmooth_2.23-24       
 [87] DBI_1.2.3                 colorspace_2.1-1         
 [89] nnet_7.3-19               tidyselect_1.2.1         
 [91] curl_6.0.1                bit_4.5.0                
 [93] compiler_4.3.2            BiocNeighbors_1.20.2     
 [95] DelayedArray_0.28.0       plotly_4.10.4            
 [97] rtracklayer_1.62.0        scales_1.3.0             
 [99] lmtest_0.9-40             digest_0.6.37            
[101] goftest_1.2-3             spatstat.utils_3.1-1     
[103] rmarkdown_2.29            XVector_0.42.0           
[105] htmltools_0.5.8.1         pkgconfig_2.0.3          
[107] sparseMatrixStats_1.14.0  fastmap_1.2.0            
[109] rlang_1.1.4               htmlwidgets_1.6.4        
[111] shiny_1.9.1               DelayedMatrixStats_1.24.0
[113] farver_2.1.2              zoo_1.8-12               
[115] jsonlite_1.8.9            BiocParallel_1.36.0      
[117] R.oo_1.27.0               BiocSingular_1.18.0      
[119] RCurl_1.98-1.16           magrittr_2.0.3           
[121] modeltools_0.2-23         GenomeInfoDbData_1.2.11  
[123] dotCall64_1.2             munsell_0.5.1            
[125] viridis_0.6.5             reticulate_1.35.0        
[127] stringi_1.8.4             zlibbioc_1.48.2          
[129] MASS_7.3-60.0.1           org.Hs.eg.db_3.18.0      
[131] plyr_1.8.9                pkgbuild_1.4.5           
[133] ggstats_0.7.0             parallel_4.3.2           
[135] listenv_0.9.1             ggrepel_0.9.6            
[137] deldir_2.0-4              Biostrings_2.70.3        
[139] splines_4.3.2             tensor_1.5               
[141] hms_1.1.3                 locfit_1.5-9.10          
[143] igraph_2.1.1              spatstat.geom_3.2-8      
[145] RcppHNSW_0.6.0            reshape2_1.4.4           
[147] ScaledMatrix_1.10.0       pkgload_1.4.0            
[149] XML_3.99-0.17             evaluate_1.0.1           
[151] scran_1.30.2              BiocManager_1.30.25      
[153] tzdb_0.4.0                httpuv_1.6.15            
[155] RANN_2.6.2                polyclip_1.10-7          
[157] future_1.34.0             scattermore_1.2          
[159] rsvd_1.0.5                xtable_1.8-4             
[161] restfulr_0.0.15           svMisc_1.2.3             
[163] RSpectra_0.16-2           later_1.3.2              
[165] viridisLite_0.4.2         AnnotationDbi_1.64.1     
[167] GenomicAlignments_1.38.2  memoise_2.0.1            
[169] beeswarm_0.4.0            tximport_1.28.0          
[171] cluster_2.1.6             timechange_0.3.0         
[173] globals_0.16.3